Firmly establishing the evidence for structural and functional plasticity in the human brain is challenging because training-related changes in MRI-measures of brain structure and function can be influenced by potential confounds such as time-of-day (TOD). Further, many previous studies have not shown compelling evidence for the specificity of effects, to both task and brain region. To address these issues, we scanned 19 healthy adults over four visits, a week apart. Each visit included scan sessions in the AM and PM. On visits 1 and 4, participants received no training allowing us to model diurnal changes in MRI measures. On visits 2 and 3, between the AM and PM scans, participants trained for 90 minutes on a right-lateralized visuospatial-learning and a left-lateralized motor sequence-learning task respectively. Participants showed significant improvement in behavioral performance in both tasks, after training. Analysis of MRI measures of brain structure (e.g. cortical thickness, fractional anisotropy) and function (e.g. resting state functional connectivity (rsFC)) revealed: significant fluctuations in MRI measures of structure and function that were related to physiological changes in CSF and/or blood flow dynamics due to TOD, rather than training. After controlling for the effect of TOD, we did not find strong evidence for task-specific changes in MRI measures of brain structure, but did find some evidence for functional changes as measured using rsFC. These results underscore the importance of controlling for potential confounds in MRI studies of training-related plasticity.